DNA Barcoding Studies Research Articles

Re-evaluating the presence of Carex microcarpa (Cyperaceae) in Italy based on herbarium material and DNA barcoding

Carex microcarpa (sect. Rhynchocystis) is a Central Mediterranean endemic known from Corsica, Sardinia and the Tuscan archipelago, that has been also reported from scattered localities in mainland Italy (Abruzzo, Lazio and Apulia). We tested by molecular means the identification of three specimens classified as C. microcarpa from continental Italy, as well as a voucher from the Montecristo island (Tuscany) and one from Sardinia, whose taxonomic identity could not be determined with certainty by morphological examination. We performed a DNA barcoding study based on four DNA regions (two nuclear, two plastid). Our results reveal that none of previous mainland Italian records corresponds to C. microcarpa, but to C. pendula, which also belong to section Rhynchocystis, and in other cases possibly to C. acutiformis, from a different species group (sect. Paludosae). The specimen from Montecristo island was confirmed to be C. microcarpa. We conclude that C. microcarpa is likely a Tyrrhenian endemic exclusively known with certainty in Corsica, Sardinia and the Tuscan Archipelago. The presence of C. microcarpa in the Italian peninsula remains highly doubtful and we recommend its exclusion from checklists. Our study highlights the utility of DNA barcoding approaches in Carex when a reliable morphology-based identification is not possible. Supplemental data for this article is available online at https://doi.org/10.1080/11263504.2021.1897703 .

Multiple drivers behind mislabeling of fish from artisanal fisheries in La Paz, Mexico.

Seafood mislabeling has the potential to mask changes in the supply of species due to overfishing, while also preventing consumers from making informed choices about the origin, quality and sustainability of their food. Thus, there is a need to understand mislabeling and analyze the potential causes behind it to propose solutions. We conducted a COI DNA barcoding study in La Paz, Baja California Sur, Mexico, with 74 samples from fish markets and 50 samples from restaurants. We identified 38 species sold under 19 commercial names, from which at least ∼80% came from local small-scale fisheries. Overall, 49 samples, representing 40% (95% CI [31.4–48.3]) were considered mislabeled in our samples. Based on analyses where species were assigned to three price categories, economic incentives were associated with approximately half of the mislabeling events observed, suggesting that other motivating factors might simultaneously be at play. Using a network approach to describe both mislabeling (when species are mislabeled as the focal species) and substitution (when the focal species is used as substitute for others), we calculated proxies for the net availability of each species in the market. We found that local fish landings were a significant predictor of the net availability of the 10 most important commercial species at retail, but this true availability was masked to the eyes of the final consumer by both mislabeling and substitution. We hypothesize that the level of supply of each species could help explain mislabeling and substitution rates, where species in low supply and high demand could show higher mislabeling rates and rarely be used as substitutes, while species in high supply and low demand could be used as substitutes for the preferred species. Other factors affecting mislabeling include national regulations that restrict the fishing or commercialization of certain species and local and global campaigns that discourage specific patterns of consumption. We discuss how these factors might influence mislabeling and propose some solutions related to communication and education efforts to this local and global challenge.

DNA barcoding of primates and the selection of molecular markers using African Great Apes as a model.

Ambiguities within species description and identification may compromise research validity. Species identification has typically been based upon morphological characteristics, yet recent technological advances have led to identifications achieved via DNA approaches, including DNA barcoding. DNA barcoding studies typically use cytochrome c oxidase subunit I (COI) as the proposed universal molecular marker for animals. Here, we test 12 mitochondrial protein coding genes for the presence of a clear barcoding gap allowing us to unequivocally define species. Using the African Great Apes as our model group, we assess this at the species (Pan troglodytes), genus (Pan) and family (Hominidae) level. Based on 279 complete mitochondrial genomes, sequences were partitioned by gene for analysis and pairwise distances were calculated. No barcoding gap was observed at the within species level, i.e., the four recognised chimpanzee taxa were not distinguishable through DNA barcoding. However, NADH dehydrogenase subunit 5 (ND5) and cytochrome c oxidase subunit II (COII) produce the largest barcoding gaps at the genus (ND5 2%, COII 0.5%) and family (ND5 1.5%, COII 0.5%) level. Rather than focusing on COI, our analysis suggests that these two genes may be more, or at least as, appropriate markers in primate species delineation, with uses in the identification of extinct and extant species. Further use may be beneficial to taxonomists, providing additional evidence and new insights for these morphologically similar species.

DNA BARCODING LIBRARY DATABASE OF AQUILARIA MEMBER AND GYRINOPS MEMBER

Aquilaria and Gyrinops are the primary agarwood producer on international trade. For authentication and standardization purposes, it is essential to carry DNA barcoding studies of these genera. DNA barcoding studies on plants need a database of several regions on the plant genome that could act as a barcoding marker. These DNA barcoding markers could be divided into Chloroplasts barcoding and Nuclear barcoding. Several markers have been used for DNA barcoding study of agarwood producer species, including trnL-trnF, matK, rbcL, rpoC1, ycf1 (Chloroplast barcoding), and ITS (Nuclear barcoding). This review breakdown the availability of those DNA barcoding markers on the online genebank database for Aquilaria and Gyrinops. Aquilaria genus has 12 species members, while Gyrinops genus has six species members. The sequence of region trnL-trnF is the only barcoding marker covering all 12 species members of Aquilaria and six species members of Gyrinops. Both ITS and matK have covered nine species among 12 total species members of Aquilaria. The rbcL, rpoC1, and ycf1, respectively, have covered eight, five, and four species members of Aquilaria. Most of the barcoding markers have covered three species members of Gyrinops except for ITS (5 species) and rpoC1 (1 species). However, Gyrinops members have no ycf1 sequence on genebank database. Based on sequence availability on the genebank database, it could be concluded that the trnL-trnF region is the most promising DNA barcoding marker for the Aquilaria and Gyrinops members especially for the phylogenetic analysis purpose.

Widespread Torix Rickettsia in New Zealand amphipods and the use of blocking primers to rescue host COI sequences

Endosymbionts and intracellular parasites are common in arthropod hosts. As a consequence, (co)amplification of untargeted bacterial sequences has been occasionally reported as a common problem in DNA barcoding. While identifying amphipod species with universal COI primers, we unexpectedly detected rickettsial endosymbionts belonging to the Torix group. To map the distribution and diversity of Rickettsia species among amphipod hosts, we conducted a nationwide molecular screening of seven families of New Zealand freshwater amphipods. In addition to uncovering a diversity of Torix Rickettsia species across multiple amphipod populations from three different families, our research indicates that: (1) detecting Torix Rickettsia with universal primers is not uncommon, (2) obtaining ‘Rickettsia COI sequences’ from many host individuals is highly likely when a population is infected, and (3) obtaining ‘host COI’ may not be possible with a conventional PCR if an individual is infected. Because Rickettsia COI is highly conserved across diverse host taxa, we were able to design blocking primers that can be used in a wide range of host species infected with Torix Rickettsia. We propose the use of blocking primers to circumvent problems caused by unwanted amplification of Rickettsia and to obtain targeted host COI sequences for DNA barcoding, population genetics, and phylogeographic studies.

<p class="Paragraph"><strong>DNA barcoding unravels three new species and a subspecies of <em>Olepa </em>Watson, 1980 (Lepidoptera, Erebidae, Arctiinae) from India, with morphotypes</strong></p>

The genus Olepa is distributed in Palearctic and Oriental regions with more species in India and Sri Lanka. In the recent studies, morphological variations within the group were well established, with couple of first set of mt COI DNA barcodes for at least three species. In the present account, three new species and a new subspecies are described from the northern Western Ghats region of Maharashtra based on mt COI DNA barcode studies. Due to high morphological divergence and complete genetic homogeneity on the mt COI DNA, four morphotypes under two species are reported. Morphological and genital characters of male and female are provided along with their respective species morphotypes for the first time under this genus from India. The genitalia and the habitus of male and female are illustrated. Preliminary phylogenetic tree based on the mt COI DNA sequences available in the GenBank for the genus with the sequences for the new species also provided and discussed. Key words: new taxa, morphotype, Maharashtra, DNA barcoding, mt COI gene

Italian odonates in the Pandora's box: A comprehensive DNA barcoding inventory shows taxonomic warnings at the Holarctic scale.

The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference data sets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658-bp 5' end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the data set to 1,294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC and bGMYC) methods was used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct molecular operational units, whereas the remaining ones were classified as 'warnings' (i.e. showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped into three categories depending on if they showed low, high or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.

First records raise questions: DNA barcoding of Odonata in the middle of the Mediterranean.

We present the results of the first-ever DNA barcoding study of odonates from the Maltese Islands. In total, 10 morphologically identified species were collected during a two-week long expedition in 2018. Eighty cytochrome c oxidase subunit I (COI) barcodes were obtained from the collected specimens. Intra- and interspecific distances ranged from 0.00% to 2.24% and 0.48% to 17.62%, respectively. Successful species identification based on ascribing a single morphological species to a single Barcode Index Number (BIN) was achieved for eight species (80%). In the case of two species, Ischnura genei and Anax parthenope, BINs were shared with other closely related species. The taxonomic status of I. genei is questionable and the phylogenetic relationship between A. imperator/parthenope is not clear. Further studies involving a series of adult specimens collected in a wide spatial range and nuclear markers are necessary to resolve these cases. Therefore, this dataset serves as an initial DNA barcode reference library for Maltese odonates, within a larger project: Aquatic Macroinvertebrates DNA Barcode Library of Malta.

The Black Sea Flexopecten species-complex (Mollusca: Bivalvia: Pectinidae): Shell morphology and 16S rDNA variation

The taxonomic status and population variability of a Black Sea scallop (Flexopecten: Mollusca, Pectinidae) was evaluated in a DNA barcoding study using the 16S ribosomal DNA gene (=16S rDNA), in conjunction with seven morphological features of the shell. We conclude that the Black Sea form represents an eastern extension of the Mediterranean scallop F. glaber (Linnaeus, 1758). It is characterized by a significant lack of genetic variability when compared to the Mediterranean form, although it does contain new haplotypes not found in that species. There is also an increase in the mismatch in the distribution of nucleotides for the Black Sea form when compared with pooled samples of Mediterranean scallop. Plausible reasons for the observed phenomena are hypothesized from the standpoint of the epigenetic theory of evolution and the time since the scallop penetrated into the Black Sea. The lack of genetic variability is potentially due to founder effect and genetic drift.

Ptomaphagus thebeatles n. sp., a previously unrecognized beetle from Europe, with remarks on urban taxonomy and recent range expansion (Coleoptera: Leiodidae)

Abstract Anthropogenic environmental change is leading to changes in distribution for many organisms. While this is frequently discussed for prominent organisms of high conservation value, the same is true for the many cryptic species that rarely figure in debates on the human impact. One such cryptic taxon is the European Ptomaphagus sericatus (Chaudoir, 1845) and related forms. During a citizen science expedition in the Vondelpark, Amsterdam, the Netherlands, we obtained two forms of this species complex. We placed the examination of these specimens in the context of a re-analysis of the species group, and, using DNA barcoding and genital study on material collected thoughout Europe, found that the P. sericatus species complex consists of three distinct, partly sympatric species, one of which was previously undescribed. On the basis of collection data, at least two species, P. medius and P. thebeatles sp. n., show signs of having recently undergone (possibly anthropogenic) range changes, with P. medius even reaching North America. We describe P. thebeatles sp. n.; we raise two subspecies, viz. P. sericatus sericatus (Chaudoir, 1854) and P. sericatus medius (Rey, 1889) to the level of species, and designate a neotype for the former; we identify P. dacicus Jeannel, 1934 and P. pyrenaeus Jeannel, 1934 as junior synonyms of P. sericatus, and P. compressitarsus (Rey, 1889) as a junior synonym of P. subvillosus Goeze, 1777; we identify P. septentrionalis Jeannel, 1934 and P. miser (Rey, 1889) as junior synonyms of P. medius; we designate lectotypes for P. medius and P. miser.

DNA barcoding and species delimitation of the Old World tooth-carps, family Aphaniidae Hoedeman, 1949 (Teleostei: Cyprinodontiformes).

The fishes, which have currently named Aphanius Nardo, 1827 are the relict of the ancient ichthyofauna of the Tethys Sea. For a long time since 1827, the genus name has been subjected to revision by several researchers using mainly morphological features. Until recently, no comprehensive single- or multi-locus DNA barcoding study has been conducted on whole members of the family Aphaniidae. In the present study, by applying four conceptually different molecular species delimitation methods, including one distance-based method, one network-based and two topology-based methods, we examined a single-locus DNA barcode library (COI) diversity for the 268 sequences within the family Aphaniidae from the Old World (57 sequences are new in the present study and 211 sequences were retrieved from NCBI database). The molecular analyses revealed a clearer picture of intra-family relationships and allowed us to clarify the generic names, and also describe a new genus for the family Aphaniidae. Results supported distinction of three major clades related to three genera within this family: i) the first clade includes the A. mento group which are placed in a new genus, Paraphanius gen. nov., found in the Orontes (= Asi) and Tigris-Euphrates River drainage, the Levant in coastal waters and the Dead Sea basin, western Jordan, and in southern Turkey in the Mediterranean basins as well as in central Turkey. This clade positioned at the base of the phylogenetic tree, (ii) the second clade contains the A. dispar-like brackish water tooth-carps which are transferred to the genus Aphaniops Hoedeman, 1951 (type species, Lebias dispar), distributed in the coastal waters around the Red Sea and the Persian Gulf basins; and (iii) the third clade, the genus Aphanius Nardo, 1827 (type species Aphanius nanus = A. fasciatus) contains all the inland and inland-related tooth-carps, which are mainly distributed in the inland waters in Turkey and Iran and also in the inland-related drainages around the Mediterranean basin.

The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material.

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.

New species of Silhouettea (Teleostei: Gobiidae) from Qeshm Island, Iran andthe DNA barcoding of the Persian Gulf and Oman Sea gobies.

Silhouettea ghazalae sp. nov. is described from Qeshm Island, Persian Gulf. Silhouettea ghazalae sp. nov. is distinguished from congeners by having: small mental fold present on chin, head length 31.4-32.4% of standard length, head width 24.5% of standard length, second dorsal fin I/11, anal fin I/13, breast with large cycloid scales, predorsal area naked, suborbital row b anteriorly beginning below anterior edge of pupil, posteriorly ending below pore β, suborbital row c anteriorly extending more than row b and posteriorly extending less than row b, suborbital row cp oblique with four papillae, body with four ill-defined midlateral blotches and the fifth a triangular mark on the caudal fin base, no clearly defined pale saddles on back, and the first dorsal fin pigmented with dots and with dark blotch present anteriorly. A key to Silhouettea species is provided. A dataset including novel and publicly available mtDNA COI sequences of 12 species from the Persian Gulf and Oman Sea gobies belonging to eight genera have been assembled in order to provide a reference dataset for DNA barcoding studies. The new species is further characterised by a minimum K2P distance of 21% to its closest relatives in our dataset, Cabillus tongarevaein the mtDNA COI barcode region.

HACSim: an R package to estimate intraspecific sample sizes for genetic diversity assessment using haplotype accumulation curves.

Assessing levels of standing genetic variation within species requires a robust sampling for the purpose of accurate specimen identification using molecular techniques such as DNA barcoding; however, statistical estimators for what constitutes a robust sample are currently lacking. Moreover, such estimates are needed because most species are currently represented by only one or a few sequences in existing databases, which can safely be assumed to be undersampled. Unfortunately, sample sizes of 5–10 specimens per species typically seen in DNA barcoding studies are often insufficient to adequately capture within-species genetic diversity. Here, we introduce a novel iterative extrapolation simulation algorithm of haplotype accumulation curves, called HACSim (Haplotype Accumulation Curve Simulator) that can be employed to calculate likely sample sizes needed to observe the full range of DNA barcode haplotype variation that exists for a species. Using uniform haplotype and non-uniform haplotype frequency distributions, the notion of sampling sufficiency (the sample size at which sampling accuracy is maximized and above which no new sampling information is likely to be gained) can be gleaned. HACSim can be employed in two primary ways to estimate specimen sample sizes: (1) to simulate haplotype sampling in hypothetical species, and (2) to simulate haplotype sampling in real species mined from public reference sequence databases like the Barcode of Life Data Systems (BOLD) or GenBank for any genomic marker of interest. While our algorithm is globally convergent, runtime is heavily dependent on initial sample sizes and skewness of the corresponding haplotype frequency distribution.

Application of rbcL in DNA barcoding of Phaleria macrocarpa (Scheff.) Boerl. and its processed commercial products

DNA barcoding is a molecular-based identification method which utilizes specific short DNA fragment known as DNA barcode. It can be used to assist species identification of specimens already lacking its original morphological traits such as processed herbal products. Phaleria macrocarpa (Scheff.) Boerl. is a plant species that originated from Malaysia and Indonesia and is locally known as God’s crown or Mahkota dewa in Malaysia. It is frequently used in Malaysian and Indonesian traditional medicines. Its fruits for example are used to treat flu, rheumatism, cancer, diabetes mellitus and hypertension. Due to its restorative properties, this plant is now commercially grown in Malaysia where its fruit is usually processed into various types of herbal products such as capsules, tea and coffee. However, due to the increasing popularity of this plant, it is important to have an effective method that can determine the authenticity of P. macrocarpa based products. In this study, the plastid rbcL barcoding gene was used to verify the authenticity of two local processed products claimed to have been made using the fruit of P. macrocarpa. The amplification of the partial rbcL gene was done via Polymerase Chain Reaction (PCR) using KAPA3G Plant PCR Kit. The DNA sequencing results were trimmed using ChromasPro before being aligned using ClustalW which was included in MEGA5. Species verification using the BLASTn search tool revealed that the species contained in both products were found to be P. macrocarpa. Phylogenetic reconstruction via Neighbour-Joining tree using partial rbcL gene amplified from the two tested products and fresh Mahkota dewa plant also revealed high similarity, supporting the BLASTn analysis. In conclusion, this study has shown that the rbcL barcode is suitable to be used to determine the authenticity of processed commercial products of P. macrocarpa. Furthermore, we believe that there is currently no DNA barcoding study that focuses solely on P. macrocarpa and its commercial products. To the extent of our abilities, we believe that there is currently no DNA barcoding study that focuses solely on P. macrocarpa and its commercial products, using the KAPA3G Plant PCR kit. We propose that to determine the authenticity of any P. macrcarpa based products; the rbcL barcode can be used with the KAPA3G Plant PCR kit, especially in laboratories that do not have access to liquid nitrogen.

The species identification problem in mirids (Hemiptera: Heteroptera) highlighted by DNA barcoding and species delimitation studies

Due to the difficulties associated with detecting and correctly identifying mirids, developing an accurate species identification approach is crucial, especially for potential harmful species. Accurate identification is often hampered by inadequate morphological key characters, invalid and/or outdated systematics, and biases in the molecular data available in public databases. This study aimed to verify whether molecular characterization (i.e. DNA barcoding) is able to identify mirid species of economic relevance and if species delimitation approaches are reliable tools for species discrimination. Cytochrome c oxydase 1 (cox1) data from public genetic databases were compared with new data obtained from mirids sampled in different Italian localities, including an old specimen from private collection, showing contrasting results. Based on the DNA barcoding approach, for the genus Orthops, all sequences were unambiguously assigned to the same species, while in Adelphocoris, Lygus and Trigonotylus there were over-descriptions and/or misidentifications of species. On the other hand, in Polymerus and Deraeocoris there was an underestimation of the taxonomic diversity. The present study highlighted an important methodological problem: DNA barcoding can be a good tool for pest identification and discrimination, but the taxonomic unreliability of public DNA databases can make this method useless or even misleading.

DNA barcoding of endemic and endangered orchids of India: A molecular method of species identification

Background: Orchids are economically important, particularly in horticulture, floristry, pharmaceutical, and fragrance industries. India is a paradise for 1256 orchids, of which 31% (388 species) are endemic. Although Indian orchids are known in floristry, there is still a lot of room to use their bioactive compounds to promote their commercialization. Easy and accurate identification is first step towards conservation and commercial cultivation of endemic and endangered orchid species. This requirement can be accomplished using DNA barcoding technique. Materials and Methods: A total of 62 samples belonging to 35 species, 7 genera were collected for DNA barcoding studies. Evolutionary divergences and barcoding gap were calculated using MEGA-X software to screen the most suitable barcode region among the ITS, matK, rbcL , and trnH-psbA loci. BLAST analysis was used to identify barcoding locus presenting maximum species resolution. Phylogenetic analyses were performed to test harmony between barcoding and taxonomy. Results: We have generated 133 barcoding sequences, out of which, 46 sequences were found unique and new to GenBank database. Evolutionary divergence analysis showed the best result for ITS , where intra-specific and inter-specific divergence ranged between 0.0000–0.0300 and 0.0322–0.3765 correspondingly. It indicated clear barcoding gap, which was sufficient to robustly infer identities for taxa. BLAST-based evaluation concluded that largest number of barcode sequences (94.64%) could be identified using ITS locus followed by rbcL (78.69%) and matK (51.61%). In addition, the optimal phylogenetic tree was established using the ITS locus sequences, which complemented the orchid taxonomy. Conclusion: This study recommends ITS as best single locus barcoding region for identifying the orchids of India.

Species delimitation and evolutionary relationships among Phoebis New World sulphur butterflies (Lepidoptera, Pieridae, Coliadinae)

ABSTRACTThe most accepted taxonomic treatment of the New World sulphurs of the genus Phoebis Hübner, [1819] recognizes 16 species including those in the current synonyms Aphrissa and Rhabdodryas. This total conflicts with the results of several recent pierid DNA barcode studies across the Neotropics. We used a five‐locus dataset to carry out species delimitation analyses using the coalescence‐based method implemented in bpp software. After testing the resulting species hypotheses using marginal likelihood estimates, we inferred their phylogenetic relationships and performed an ancestral range reconstruction with biogeobears. Our analyses recovered two different hypotheses, 26 and 24 species, that scored the highest marginal likelihood estimate. Differences between these two hypotheses, when reconciled with barcode clusters and morphology, indicated that 24 is the most likely number of species. Phoebis neocypris stat. rev., Phoebis rurina stat. rev., Phoebis virgo stat. rev., Phoebis marcellina stat. rev., Phoebis thalestris stat. rev., and Phoebis rorata stat. rev. are raised to the species rank. We dated the crown age of Phoebis to the mid‐Miocene, with the islands of the Greater Antilles as the most probable ancestral range. Three main clades of Phoebis diverged early in the evolutionary history of the genus, but most extant species‐level diversity arose after the Pliocene–Pleistocene boundary. Our analyses recovered alternate range expansions and contractions, and dispersal from the islands to the continent and back, in the three main clades. Both sympatric and allopatric speciation seem to have shaped the current species richness.

Broad North Atlantic distribution of a meiobenthic annelid – against all odds

DNA barcoding and population genetic studies have revealed an unforeseen hidden diversity of cryptic species among microscopic marine benthos, otherwise exhibiting highly similar and simple morphologies. This has led to a paradigm shift, rejecting cosmopolitism of marine meiofauna until genetically proven and challenging the “Everything is Everywhere, but the environment selects” hypothesis that claims ubiquitous distribution of microscopic organisms. With phylogenetic and species delimitation analyses of worldwide genetic samples of the meiofaunal family Dinophilidae (Annelida) we here resolve three genera within the family and showcase an exceptionally broad, boreal, North Atlantic distribution of a single microscopic marine species with no obvious means of dispersal besides vicariance. With its endobenthic lifestyle, small size, limited migratory powers and lack of pelagic larvae, the broad distribution of Dinophilus vorticoides seems to constitute a “meiofaunal paradox”. This species feasts in the biofilm among sand grains, but also on macroalgae and ice within which it can likely survive long-distance rafting dispersal due to its varying lifecycle stages; eggs encapsulated in cocoons and dormant encystment stages. Though often neglected and possibly underestimated among marine microscopic species, dormancy may be a highly significant factor for explaining wide distribution patterns and a key to solving this meiofaunal paradox.

DNA barcode and phylogenetic study of the tribe Desmodieae (Fabaceae) in Korea

본 연구에서는 DNA 바코드, 즉 엽록체 DNA의 rbcL, matK와 핵 리보솜 DNA의 ITS 염기서열을 이용하여 한국산 ë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ì¡± 식물들의 ì¢ ì‹ë³„ì„ 실시하였다. 총 5개속 25분류군(총 75개체)의 식물에 대한 염기서열이 ë°í˜€ì¡Œê³ , DNA 바코드 구간 조합에 따라 neighbor-joining 계통수들이 작성되었다. ê·¸ ê²°ê³¼, ì¢ ì‹ë³„ë¥ ì€ DNA 바코드 3개의 구간을 모두 사용하였을 때 가장 높게 나타났다(72%). rbcL+matK+ITS 계통수에서 본 족의 두 개의 아족과 다섯 속들은 단계통군으로 ìœ ì§‘ë˜ì—ˆë‹¤. ë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ì•„ì¡±êµ°ì—ì„œ 도둑놈의 ê°ˆê³ ë¦¬ì†ê³¼ ê°ˆê³ ë¦¬ì†ì´ 된장풀속보다 더 가깝게 묶였다. ê°ˆê³ ë¦¬ì†êµ°ì—ì„œ í°ë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ëŠ” ê°œë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ 복합체의 자매군으로 í˜•ì„±ë˜ì—ˆê³ , ê°œë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ì˜ ì¢ ë‚´ë¶„ë¥˜êµ°ë“¤ì€ 각각 단계통을 형성하였다. 특히 í˜•íƒœì  변이로 인해 ë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ì˜ ë³€ì¢ ë˜ëŠ” ê°œë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ì™€ì˜ 중간형으로 인식된 바 있는 ê¸´ë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ëŠ” ê°œë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ì™€ 가장 가깝게 묶였다. 한편 ë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ì˜ ë³€ì¢ ì´ë‚˜ ì´ëª ìœ¼ë¡œ 인식되어온 ì• ê¸°ë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ëŠ” ë³€ì¢ ìœ¼ë¡œ 판단되었다. 싸리아족군의 경우, 매듭풀속 분류군들은 계통수상에서 각각 단계통으로 지지되었으나, 싸리속의 식물 16분류군 중 9분류군만 ì¢ ì‹ë³„ì´ 가능하였다. 특히 ì‹¸ë¦¬ì†ë‚´ë• ë¹„ìˆ˜ë¦¬ì ˆë³´ë‹¤ ì‹¸ë¦¬ì ˆì—ì„œ 낮은 ì¢ íŒë³„ 해상능이 나타났다(ì‹¸ë¦¬ì ˆ=28.5%, ë¹„ìˆ˜ë¦¬ì ˆ=77.8%). 싸리속 식물 중에 비수리는 계통수상에서 í˜•íƒœì ìœ¼ë¡œ ìœ ì‚¬í•œ 자주비수리와 확연히 구분되었다. ìž¡ì¢ ìœ¼ë¡œë„ 인식된 바 있는 해변싸리와 청비수리 중, 해변싸리는 ë ë¦½ì¢ ìœ¼ë¡œ 판단되었다. 반면 청비수리는 ìž¡ì¢ ì—¬ë¶€ë¥¼ íŒë‹¨í• ìˆ˜ëŠ” 없었지만, ë• ë¹„ìˆ˜ë¦¬ì™€ 근연 관계에 있는 것으로 사료된다. 주요어: ë„ë‘‘ë†ˆì˜ê°ˆê³ ë¦¬ì¡±, ì¢ ì‹ë³„, DNA 바코드 rbcL, matK, ITS